private void getBondsInRing(IAtomContainer mol, IRing ring, int[] bonds)
{
for (int i = 0; i < ring.getBondCount(); i++)
{
int m = mol.getBondNumber(ring.getBondAt(i));
bonds[m] = 1;
}
}
public virtual void identifyBonds()
{
IAtomContainer spt = getSpanningTree();
IRing ring;
int nBasicRings = 0;
for (int i = 0; i < E; i++)
{
if (!bondsInTree[i])
{
ring = getRing(spt, molecule.getBondAt(i));
for (int b = 0; b < ring.getBondCount(); b++)
{
int m = molecule.getBondNumber(ring.getBondAt(b));
cb[nBasicRings][m] = 1;
}
nBasicRings++;
}
}
spt = null; ring = null;
bondsAcyclicCount = 0; bondsCyclicCount = 0;
for (int i = 0; i < E; i++)
{
int s = 0;
for (int j = 0; j < nBasicRings; j++)
{
s += cb[j][i];
}
switch (s)
{
//acyclic bond
case (0):
{
bondsAcyclicCount++; break;
}
case (1):
{
bondsCyclicCount++; break;
}
default:
{
bondsCyclicCount++;
}
break;
}
}
}
/// <summary> Says if an atom is the end of a double bond configuration
///
/// </summary>
/// <param name="atom"> The atom which is the end of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not end of configuration, true=is
/// </returns>
private static bool isEndOfDoubleBond(IAtomContainer container, IAtom atom, IAtom parent, bool[] doubleBondConfiguration)
{
if (container.getBondNumber(atom, parent) == -1 || doubleBondConfiguration.Length <= container.getBondNumber(atom, parent) || !doubleBondConfiguration[container.getBondNumber(atom, parent)])
{
return(false);
}
int lengthAtom = container.getConnectedAtoms(atom).Length + atom.getHydrogenCount();
int lengthParent = container.getConnectedAtoms(parent).Length + parent.getHydrogenCount();
if (container.getBond(atom, parent) != null)
{
if (container.getBond(atom, parent).Order == CDKConstants.BONDORDER_DOUBLE && (lengthAtom == 3 || (lengthAtom == 2 && atom.Symbol.Equals("N"))) && (lengthParent == 3 || (lengthParent == 2 && parent.Symbol.Equals("N"))))
{
IAtom[] atoms = container.getConnectedAtoms(atom);
IAtom one = null;
IAtom two = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && one == null)
{
one = atoms[i];
}
else if (atoms[i] != parent && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if ((one != null && two == null && atom.Symbol.Equals("N") && System.Math.Abs(giveAngleBothMethods(parent, atom, one, true)) > System.Math.PI / 10) || (!atom.Symbol.Equals("N") && one != null && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)])))
{
return(true);
}
else
{
return(false);
}
}
}
return(false);
}
private void getBondsInRing(IAtomContainer mol, IRing ring, int[] bonds)
{
for (int i = 0; i < ring.getBondCount(); i++)
{
int m = mol.getBondNumber(ring.getBondAt(i));
bonds[m] = 1;
}
}
/// <summary> Says if an atom is the start of a double bond configuration
///
/// </summary>
/// <param name="a"> The atom which is the start of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not start of configuration, true=is
/// </returns>
private bool isStartOfDoubleBond(IAtomContainer container, IAtom a, IAtom parent, bool[] doubleBondConfiguration)
{
int lengthAtom = container.getConnectedAtoms(a).Length + a.getHydrogenCount();
if (lengthAtom != 3 && (lengthAtom != 2 && (System.Object)a.Symbol != (System.Object)("N")))
{
return (false);
}
IAtom[] atoms = container.getConnectedAtoms(a);
IAtom one = null;
IAtom two = null;
bool doubleBond = false;
IAtom nextAtom = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && container.getBond(atoms[i], a).Order == CDKConstants.BONDORDER_DOUBLE && isEndOfDoubleBond(container, atoms[i], a, doubleBondConfiguration))
{
doubleBond = true;
nextAtom = atoms[i];
}
if (atoms[i] != nextAtom && one == null)
{
one = atoms[i];
}
else if (atoms[i] != nextAtom && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if (one != null && ((!a.Symbol.Equals("N") && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)]) && doubleBond && doubleBondConfiguration[container.getBondNumber(a, nextAtom)]) || (doubleBond && a.Symbol.Equals("N") && System.Math.Abs(BondTools.giveAngleBothMethods(nextAtom, a, parent, true)) > System.Math.PI / 10)))
{
return (true);
}
else
{
return (false);
}
}
/// <summary> Says if an atom is the end of a double bond configuration
///
/// </summary>
/// <param name="atom"> The atom which is the end of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not end of configuration, true=is
/// </returns>
private bool isEndOfDoubleBond(IAtomContainer container, IAtom atom, IAtom parent, bool[] doubleBondConfiguration)
{
if (container.getBondNumber(atom, parent) == -1 || doubleBondConfiguration.Length <= container.getBondNumber(atom, parent) || !doubleBondConfiguration[container.getBondNumber(atom, parent)])
{
return false;
}
int lengthAtom = container.getConnectedAtoms(atom).Length + atom.getHydrogenCount();
int lengthParent = container.getConnectedAtoms(parent).Length + parent.getHydrogenCount();
if (container.getBond(atom, parent) != null)
{
if (container.getBond(atom, parent).Order == CDKConstants.BONDORDER_DOUBLE && (lengthAtom == 3 || (lengthAtom == 2 && atom.Symbol.Equals("N"))) && (lengthParent == 3 || (lengthParent == 2 && parent.Symbol.Equals("N"))))
{
IAtom[] atoms = container.getConnectedAtoms(atom);
IAtom one = null;
IAtom two = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && one == null)
{
one = atoms[i];
}
else if (atoms[i] != parent && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if ((one != null && two == null && atom.Symbol.Equals("N") && System.Math.Abs(BondTools.giveAngleBothMethods(parent, atom, one, true)) > System.Math.PI / 10) || (!atom.Symbol.Equals("N") && one != null && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)])))
{
return (true);
}
else
{
return (false);
}
}
}
return (false);
}
/// <summary> This makes a map of matching atoms out of a map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
///
/// </summary>
/// <param name="l"> The list produced by the getMap method.
/// </param>
/// <param name="g1"> The first atom container.
/// </param>
/// <param name="g2"> The second one (first and second as in getMap)
/// </param>
/// <returns> The mapping found projected on g1. This is a List of RMap objects containing Ids of matching atoms.
/// </returns>
public static System.Collections.IList makeAtomsMapOfBondsMap(System.Collections.IList l, IAtomContainer g1, IAtomContainer g2)
{
if (l == null)
{
return(l);
}
IBond[] bonds1 = g1.Bonds;
IBond[] bonds2 = g2.Bonds;
System.Collections.IList result = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int i = 0; i < l.Count; i++)
{
IBond bond1 = bonds1[((RMap)l[i]).Id1];
IBond bond2 = bonds2[((RMap)l[i]).Id2];
IAtom[] atom1 = bond1.getAtoms();
IAtom[] atom2 = bond2.getAtoms();
for (int j = 0; j < 2; j++)
{
IBond[] bondsConnectedToAtom1j = g1.getConnectedBonds(atom1[j]);
for (int k = 0; k < bondsConnectedToAtom1j.Length; k++)
{
if (bondsConnectedToAtom1j[k] != bond1)
{
IBond testBond = bondsConnectedToAtom1j[k];
for (int m = 0; m < l.Count; m++)
{
IBond testBond2;
if (((RMap)l[m]).Id1 == g1.getBondNumber(testBond))
{
testBond2 = bonds2[((RMap)l[m]).Id2];
for (int n = 0; n < 2; n++)
{
System.Collections.IList bondsToTest = g2.getConnectedBondsVector(atom2[n]);
if (bondsToTest.Contains(testBond2))
{
RMap map;
if (j == n)
{
map = new RMap(g1.getAtomNumber(atom1[0]), g2.getAtomNumber(atom2[0]));
}
else
{
map = new RMap(g1.getAtomNumber(atom1[1]), g2.getAtomNumber(atom2[0]));
}
if (!result.Contains(map))
{
result.Add(map);
}
RMap map2;
if (j == n)
{
map2 = new RMap(g1.getAtomNumber(atom1[1]), g2.getAtomNumber(atom2[1]));
}
else
{
map2 = new RMap(g1.getAtomNumber(atom1[0]), g2.getAtomNumber(atom2[1]));
}
if (!result.Contains(map2))
{
result.Add(map2);
}
}
}
}
}
}
}
}
}
return(result);
}
/// <summary> Says if an atom is the start of a double bond configuration
///
/// </summary>
/// <param name="a"> The atom which is the start of configuration
/// </param>
/// <param name="container"> The atomContainer the atom is in
/// </param>
/// <param name="parent"> The atom we came from
/// </param>
/// <param name="doubleBondConfiguration"> The array indicating where double bond
/// configurations are specified (this method ensures that there is
/// actually the possibility of a double bond configuration)
/// </param>
/// <returns> false=is not start of configuration, true=is
/// </returns>
private static bool isStartOfDoubleBond(IAtomContainer container, IAtom a, IAtom parent, bool[] doubleBondConfiguration)
{
int lengthAtom = container.getConnectedAtoms(a).Length + a.getHydrogenCount();
if (lengthAtom != 3 && (lengthAtom != 2 && (System.Object)a.Symbol != (System.Object)("N")))
{
return(false);
}
IAtom[] atoms = container.getConnectedAtoms(a);
IAtom one = null;
IAtom two = null;
bool doubleBond = false;
IAtom nextAtom = null;
for (int i = 0; i < atoms.Length; i++)
{
if (atoms[i] != parent && container.getBond(atoms[i], a).Order == CDKConstants.BONDORDER_DOUBLE && isEndOfDoubleBond(container, atoms[i], a, doubleBondConfiguration))
{
doubleBond = true;
nextAtom = atoms[i];
}
if (atoms[i] != nextAtom && one == null)
{
one = atoms[i];
}
else if (atoms[i] != nextAtom && one != null)
{
two = atoms[i];
}
}
System.String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
if (one != null && ((!a.Symbol.Equals("N") && two != null && !morgannumbers[container.getAtomNumber(one)].Equals(morgannumbers[container.getAtomNumber(two)]) && doubleBond && doubleBondConfiguration[container.getBondNumber(a, nextAtom)]) || (doubleBond && a.Symbol.Equals("N") && System.Math.Abs(giveAngleBothMethods(nextAtom, a, parent, true)) > System.Math.PI / 10)))
{
return(true);
}
else
{
return(false);
}
}
/// <summary> This makes a map of matching atoms out of a map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
///
/// </summary>
/// <param name="l"> The list produced by the getMap method.
/// </param>
/// <param name="g1"> The first atom container.
/// </param>
/// <param name="g2"> The second one (first and second as in getMap)
/// </param>
/// <returns> The mapping found projected on g1. This is a List of RMap objects containing Ids of matching atoms.
/// </returns>
public static System.Collections.IList makeAtomsMapOfBondsMap(System.Collections.IList l, IAtomContainer g1, IAtomContainer g2)
{
if (l == null)
return (l);
IBond[] bonds1 = g1.Bonds;
IBond[] bonds2 = g2.Bonds;
System.Collections.IList result = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int i = 0; i < l.Count; i++)
{
IBond bond1 = bonds1[((RMap)l[i]).Id1];
IBond bond2 = bonds2[((RMap)l[i]).Id2];
IAtom[] atom1 = bond1.getAtoms();
IAtom[] atom2 = bond2.getAtoms();
for (int j = 0; j < 2; j++)
{
IBond[] bondsConnectedToAtom1j = g1.getConnectedBonds(atom1[j]);
for (int k = 0; k < bondsConnectedToAtom1j.Length; k++)
{
if (bondsConnectedToAtom1j[k] != bond1)
{
IBond testBond = bondsConnectedToAtom1j[k];
for (int m = 0; m < l.Count; m++)
{
IBond testBond2;
if (((RMap)l[m]).Id1 == g1.getBondNumber(testBond))
{
testBond2 = bonds2[((RMap)l[m]).Id2];
for (int n = 0; n < 2; n++)
{
System.Collections.IList bondsToTest = g2.getConnectedBondsVector(atom2[n]);
if (bondsToTest.Contains(testBond2))
{
RMap map;
if (j == n)
{
map = new RMap(g1.getAtomNumber(atom1[0]), g2.getAtomNumber(atom2[0]));
}
else
{
map = new RMap(g1.getAtomNumber(atom1[1]), g2.getAtomNumber(atom2[0]));
}
if (!result.Contains(map))
{
result.Add(map);
}
RMap map2;
if (j == n)
{
map2 = new RMap(g1.getAtomNumber(atom1[1]), g2.getAtomNumber(atom2[1]));
}
else
{
map2 = new RMap(g1.getAtomNumber(atom1[0]), g2.getAtomNumber(atom2[1]));
}
if (!result.Contains(map2))
{
result.Add(map2);
}
}
}
}
}
}
}
}
}
return (result);
}